GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Trp_syntA - Tryptophan synthase alpha chain
Pfam: PF00290 (v27) Consensus Sequence
Download Alignment
(Note: includes all positions in family; we filtered this alignment to remove sites that had > 75% gaps before running GREMLIN. )
Clan: CL0036
Length: 259
Sequences: 4794
Seq/Len: 18.51
HH_delta: 0.011 (20Jul13)
GREMLIN Results:
Residue pairs sorted by strength in covariance:

Legend: The darker and larger the blue dots, the higher strength in covariance. Below we provide the list of the top [1.5 x length] gremlin predictions, sequence seperation > 3. The i and j are positions as given in the consensus sequence. Show Scaled Distribution

ij Raw Score Scaled Score
82_R117_D0.879913.183
25_T28_E0.746892.702
213_A223_V0.731182.645
22_D25_T0.729352.638
239_D242_K0.721342.609
34_E88_I0.65842.382
207_I216_L0.640642.317
188_E191_K0.60632.193
242_K246_E0.6042.185
27_L80_E0.582122.106
31_K35_E0.577022.087
75_F114_A0.57632.085
109_K139_H0.572182.070
14_P38_A0.565762.046
106_R110_E0.542951.964
245_K249_E0.54261.963
241_E245_K0.539471.951
110_E113_E0.537911.946
109_K113_E0.537681.945
34_E87_D0.530361.918
126_P158_K0.530221.918
202_A222_G0.529831.916
76_E79_K0.527631.909
32_A36_A0.525911.902
136_A143_L0.522441.890
133_R137_K0.521291.886
153_E192_R0.519421.879
31_K85_E0.487291.763
232_I243_F0.480921.740
30_L41_I0.477471.727
154_E157_K0.475941.722
157_K196_H0.473591.713
135_A138_K0.45661.652
134_E138_K0.455971.649
108_F136_A0.45281.638
79_K113_E0.441391.597
194_K201_V0.439971.591
95_Y127_E0.43451.572
35_E248_K0.425731.540
30_L81_I0.425441.539
35_E241_E0.425121.538
137_K164_S0.424351.535
109_K135_A0.424081.534
129_S145_P0.407671.475
194_K221_D0.403621.460
76_E80_E0.401011.451
128_E131_E0.39841.441
36_A248_K0.394671.428
27_L31_K0.387841.403
242_K245_K0.386271.397
184_D215_K0.382661.384
243_F246_E0.381991.382
28_E31_K0.378871.370
203_V220_A0.374011.353
209_T212_Q0.373781.352
133_R143_L0.371461.344
203_V216_L0.363381.314
34_E86_P0.358971.298
11_A222_G0.358771.298
112_K139_H0.353211.278
13_I202_A0.351971.273
110_E114_A0.349871.266
43_I78_V0.349471.264
208_S231_K0.345271.249
153_E157_K0.343191.241
105_E135_A0.342381.238
125_P128_E0.341921.237
40_I222_G0.333041.205
120_I166_F0.331241.198
31_K34_E0.324581.174
207_I213_A0.324531.174
211_E215_K0.324121.172
202_A224_I0.323591.170
191_K195_K0.320841.161
200_P221_D0.32021.158
108_F132_L0.317581.149
28_E32_A0.31741.148
187_K191_K0.316841.146
55_P95_Y0.315571.141
150_T173_M0.314741.138
147_V156_I0.312711.131
208_S212_Q0.312691.131
130_E134_E0.311341.126
119_L141_L0.308651.116
40_I91_V0.308471.116
106_R109_K0.306891.110
13_I40_I0.305081.104
194_K197_T0.303891.099
216_L220_A0.302481.094
229_F247_L0.299451.083
131_E135_A0.29931.083
120_I146_L0.299211.082
111_A141_L0.297671.077
187_K215_K0.297221.075
142_D164_S0.29661.073
79_K114_A0.296491.072
240_A244_L0.29611.071
111_A116_V0.295051.067
192_R195_K0.294961.067
123_D155_R0.292331.057
133_R163_A0.291691.055
131_E134_E0.291181.053
78_V90_I0.287761.041
75_F110_E0.287511.040
130_E162_Q0.284031.027
157_K192_R0.283291.025
135_A139_H0.282441.022
166_F222_G0.281421.018
43_I90_I0.278361.007
225_V228_A0.278091.006
167_I193_I0.27691.002
193_I196_H0.275820.998
185_E188_E0.275810.998
246_E249_E0.274640.993
232_I238_D0.273650.990
212_Q215_K0.270630.979
200_P222_G0.269620.975
108_F119_L0.267530.968
208_S228_A0.267250.967
153_E191_K0.265260.959
137_K143_L0.265120.959
216_L223_V0.264350.956
124_L151_T0.261710.947
133_R162_Q0.260580.943
93_M120_I0.259770.940
148_A173_M0.258190.934
178_S182_L0.257070.930
192_R196_H0.2560.926
32_A241_E0.255160.923
211_E214_K0.253850.918
121_I132_L0.252050.912
158_K161_K0.251840.911
80_E84_K0.251470.910
172_R179_R0.250270.905
143_L164_S0.248820.900
153_E195_K0.248370.898
15_Y44_G0.24720.894
207_I223_V0.247080.894
118_G142_D0.246430.891
112_K140_G0.246170.890
217_A223_V0.242950.879
190_I203_V0.240060.868
31_K84_K0.239720.867
39_D248_K0.238930.864
179_R182_L0.236880.857
32_A240_A0.236060.854
132_L135_A0.234220.847
121_I129_S0.233230.844
26_T30_L0.233190.843
118_G166_F0.231390.837
158_K162_Q0.22990.832
34_E37_G0.227790.824
112_K141_L0.226320.819
108_F139_H0.225510.816
79_K84_K0.223170.807
23_L27_L0.220510.798
157_K161_K0.219270.793
196_H201_V0.219050.792
215_K218_A0.218560.791
108_F135_A0.216660.784
177_G226_G0.21650.783
32_A248_K0.215860.781
188_E192_R0.21540.779
212_Q216_L0.214590.776
77_L80_E0.213880.774
34_E41_I0.211470.765
107_F111_A0.210490.761
177_G206_G0.209970.759
16_I29_I0.209360.757
121_I143_L0.208010.752
244_L248_K0.206430.747
109_K112_K0.206280.746
144_I166_F0.204820.741
40_I118_G0.20440.739
137_K165_G0.203410.736
75_F111_A0.203180.735
108_F141_L0.202660.733
32_A35_E0.202470.732
152_P155_R0.2010.727
160_A196_H0.200420.725
228_A232_I0.20030.725
160_A167_I0.199310.721
145_P163_A0.198950.720
40_I166_F0.196540.711
240_A243_F0.196180.710
208_S211_E0.195680.708
187_K218_A0.195190.706
89_P117_D0.194040.702
85_E90_I0.193620.700
126_P145_P0.19360.700
11_A39_D0.192810.697
156_I193_I0.191710.693
108_F112_K0.190190.688
33_L38_A0.189810.687
82_R90_I0.189720.686
30_L90_I0.189340.685
56_V178_S0.189310.685
184_D188_E0.188350.681
239_D243_F0.188070.680
42_E204_G0.187620.679
119_L143_L0.18750.678
27_L85_E0.186430.674
145_P159_I0.186170.673
36_A241_E0.185790.672
41_I88_I0.185260.670
53_D56_V0.184720.668
89_P118_G0.183550.664
193_I201_V0.183280.663
134_E162_Q0.18310.662
32_A239_D0.182820.661
113_E139_H0.182720.661
29_I247_L0.182570.660
27_L30_L0.182440.660
30_L86_P0.181560.657
178_S231_K0.179890.651
132_L136_A0.179250.648
24_E27_L0.179080.648
209_T246_E0.178520.646
118_G200_P0.178370.645
52_A205_F0.178360.645
79_K110_E0.177760.643
147_V151_T0.177110.641
175_V201_V0.177030.640
78_V116_V0.176840.640
189_F192_R0.176460.638
54_G75_F0.17560.635
232_I246_E0.174950.633
209_T243_F0.174150.630
190_I201_V0.174030.629
137_K163_A0.173190.626
105_E132_L0.172880.625
157_K160_A0.172560.624
186_L189_F0.172380.624
179_R212_Q0.172240.623
129_S159_I0.172240.623
81_I90_I0.171790.621
213_A225_V0.171510.620
32_A244_L0.170460.617
33_L229_F0.169930.615
150_T159_I0.169780.614
179_R183_P0.169370.613
40_I202_A0.169240.612
77_L81_I0.169050.611
104_I124_L0.16760.606
93_M122_P0.167430.606
31_K86_P0.167310.605
26_T43_I0.167150.605
190_I194_K0.166830.603
79_K161_K0.166140.601
52_A57_I0.16570.599
23_L76_E0.165450.598
81_I86_P0.164570.595
23_L26_T0.164530.595
176_T204_G0.164450.595
91_V122_P0.164420.595
16_I26_T0.163920.593
18_A77_L0.16390.593
118_G222_G0.163610.592
27_L77_L0.16360.592
197_T201_V0.163090.590
186_L190_I0.163070.590
29_I244_L0.163020.590
28_E35_E0.162990.590
30_L88_I0.162860.589
94_T107_F0.162630.588
189_F220_A0.162090.586
39_D89_P0.161940.586
176_T227_S0.161760.585
214_K218_A0.161640.585
44_G204_G0.161530.584
85_E238_D0.161230.583
75_F92_L0.160950.582
11_A40_I0.160930.582
25_T29_I0.160040.579
12_L244_L0.159610.577
178_S226_G0.159490.577
91_V146_L0.159110.576
121_I124_L0.159030.575
93_M224_I0.159010.575
11_A221_D0.158590.574
119_L136_A0.158120.572
126_P162_Q0.157190.569
142_D200_P0.156610.566
12_L223_V0.156150.565
126_P161_K0.156140.565
39_D220_A0.155790.564
18_A227_S0.155320.562
122_P224_I0.15530.562
129_S133_R0.155290.562
14_P33_L0.154980.561
12_L229_F0.154950.560
111_A119_L0.154810.560
159_I162_Q0.154780.560
121_I145_P0.154680.560
190_I193_I0.154330.558
203_V207_I0.154110.557
Legend: The value of the raw score is the function of the learning procedure, L2 normalization and APC (entropic) correction. These are to be used for relative ranking only.
HHsearch Results:
Top (length/2) GREMLIN results overlayed on top 10 PDB hits:

Legend: The grey circles underneath are pdb residue contacts (min distance < 5 Angstroms). The coloring of these circles is based on HHsearch results which uses the overall probability, per-site alignment prob and agreement of top hits weighted by HHsearch score (Note we only consider monomeric contacts, there might be homo-oligomeric contacts in the pdb that are not shown.)
PDB Cov Prob HH_delta
3vndA0.99611000.011
3navA11000.021
3thaA0.95751000.054
1qopA0.99611000.137
1ujpA0.95751000.142
2ekcA0.9731000.155
1rd5A0.97681000.217
1geqA0.94591000.295
1tqjA0.84561000.4
3inpA0.84171000.422

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